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PubMed2026

Population genomics of Plasmodium malariae from 4 African countries.

BACKGROUNDMalaria caused by Plasmodium malariae is geographically widespread and sometimes associated with prolonged infection, yet little is known about its genomic epidemiology.METHODSWe performed hybrid capture and whole-genome sequencing of 77 isolates collected from Cameroon (n = 7), the Democratic Republic of the Congo (n = 16), Nigeria (n = 4), and Tanzania (n = 50) between 2015 and 2021, analyzing parasite genetic population structure and demography.RESULTSThere is no evidence of geographic population structure. Nucleotide diversity was significantly lower than in colocalized P. falciparum isolates, while linkage disequilibrium was significantly higher. Genome-wide selection scans identified no erythrocyte invasion ligands or antimalarial resistance orthologs as top hits; however, targeted analyses of these loci revealed evidence of selective sweeps around 4 erythrocyte invasion ligands and 6 antimalarial resistance orthologs. Demographic inference modeling suggests that African P. malariae is recovering from a bottleneck.CONCLUSIONP. malariae is genomically atypical among human Plasmodium spp. and lacks strong population structure in Africa. The low diversity has potential impacts on understanding persistent versus new infection through genomic epidemiology.FUNDINGBill & Melinda Gates Foundation (grant 002202), USAID/PMI through Jhpiego and CDC, NIH (T32AI007151, T32AI070114, R01AI107949, R01AI129812, R21 AI148579, R01AI137395, R21AI152260, R01AI132547, and K24AI134990), and the DELTAS Africa initiative (DELGEME grant 107740/Z/15/Z).

Plasmodium malariae↗
PubMed2005

Evolution of genetic potential.

Organisms employ a multitude of strategies to cope with the dynamical environments in which they live. Homeostasis and physiological plasticity buffer changes within the lifetime of an organism, while stochastic developmental programs and hypermutability track changes on longer time-scales. An alternative long-term mechanism is "genetic potential"--a heightened sensitivity to the effects of mutation that facilitates rapid evolution to novel states. Using a transparent mathematical model, we illustrate the concept of genetic potential and show that as environmental variability decreases, the evolving population reaches three distinct steady state conditions: (1) organismal flexibility, (2) genetic potential, and (3) genetic robustness. As a specific example of this concept we examine fluctuating selection for hydrophobicity in a single amino acid. We see the same three stages, suggesting that environmental fluctuations can produce allele distributions that are distinct not only from those found under constant conditions, but also from the transient allele distributions that arise under isolated selective sweeps.

Journal Article↗
PubMed2006

Increased nucleotide diversity with transient Y linkage in Drosophila americana.

Recombination shapes nucleotide variation within genomes. Patterns are thought to arise from the local recombination landscape, influencing the degree to which neutral variation experiences hitchhiking with selected variation. This study examines DNA polymorphism along Chromosome 4 (element B) of Drosophila americana to identify effects of hitchhiking arising as a consequence of Y-linked transmission. A centromeric fusion between the X and 4(th) chromosomes segregates in natural populations of D. americana. Frequency of the X-4 fusion exhibits a strong positive correlation with latitude, which has explicit consequences for unfused 4(th) chromosomes. Unfused Chromosome 4 exists as a non-recombining Y chromosome or as an autosome proportional to the frequency of the X-4 fusion. Furthermore, Y linkage along the unfused 4 is disrupted as a function of the rate of recombination with the centromere. Inter-population and intra-chromosomal patterns of nucleotide diversity were assayed using six regions distributed along unfused 4(th) chromosomes derived from populations with different frequencies of the X-4 fusion. No difference in overall level of nucleotide diversity was detected among populations, yet variation along the chromosome exhibits a distinct pattern in relation to the X-4 fusion. Sequence diversity is inflated at loci experiencing the strongest Y linkage. These findings are inconsistent with the expected reduction in nucleotide diversity resulting from hitchhiking due to background selection or selective sweeps. In contrast, excessive polymorphism is accruing in association with transient Y linkage, and furthermore, hitchhiking with sexually antagonistic alleles is potentially responsible.

Animals↗
PubMed2004

Evolution of specialists in an experimental microcosm.

The impact of adaptation on the persistence of a balanced polymorphism was explored using the lactose operon of Escherichia coli as a model system. Competition in chemostats for two substitutable resources, methylgalactoside and lactulose, generates stabilizing frequency-dependent selection when two different naturally isolated lac operons (TD2 and TD10) are used. The fate of this balanced polymorphism was tracked over evolutionary time by monitoring the frequency of fhuA-, a linked neutral genetic marker that confers resistance to the bacteriophage T5. In four out of nine chemostats the lac polymorphism persisted for 400-600 generations when the experiments were terminated. In the other five chemostats the fhuA polymorphism, and consequently the lac operon polymorphism, was lost between 86 and 219 generations. Four of 13 chemostat cultures monomorphic for the lac operon retained the neutral fhuA polymorphism for 450-550 generations until they were terminated; the remainder became monomorphic at fhuA between 63 and 303 generations. Specialists on each galactoside were isolated from chemostats that maintained the fhuA polymorphism, whether polymorphic or monomorphic at the lac operon. Strains isolated from three of four chemostats in which the lac polymorphism was preserved had switched their galactoside preference. Most of the chemostats where the fhuA polymorphism was lost also contained specialists. These results demonstrate that the initial polymorphism at lac was of little consequence to the outcome of long-term adaptive evolution. Instead, the fitnesses of evolved strains were dominated by mutations arising elsewhere in the genome, a fact confirmed by showing that operons isolated from their evolved backgrounds were alone unable to explain the presence of both specialists. Our results suggest that, once stabilized, ecological specialization prevented selective sweeps through the entire population, thereby promoting the maintenance of linked neutral polymorphisms.

Bacterial Outer Membrane Proteins↗
PubMed2005

Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster.

Genome-wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration, and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006N(e) generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, we find that this bottleneck model is able to predict the majority of observed features of diversity and linkage disequilibrium in the data. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it may be unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.

Animals↗
PubMed2005

The concordance of gene trees and species trees at two linked loci.

The gene genealogies of two linked loci in three species are analyzed using a series of Markov chain models. We calculate the probability that the gene tree of one locus is concordant with the species tree, given that the gene tree of the other locus is concordant. We define a threshold value of the recombination rate, r*, to be the rate for which the difference between the conditional probability of concordance and its asymptotic value is reduced to 5% of the initial difference. We find that, although r* depends in a complicated way on the times of speciation and effective population sizes, it is always relatively small, <10/N4, where N4 is the effective size of the species represented by the internal branch of the species tree. Consequently, the concordance of gene trees of neutral loci with the species tree is expected to be on roughly the same length scale on the chromosome as the extent of significant linkage disequilibrium within species unless the effective size of contemporary populations is very different from the effective sizes of their ancestral populations. Both balancing selection and selective sweeps can result in much longer genomic regions having concordant gene trees.

Animals↗
PubMed2002

Analysis of the herbicides paraquat, diquat and difenzoquat in drinking water by micellar electrokinetic chromatography using sweeping and cation selective exhaustive injection.

Optimum conditions for the determination of the herbicides paraquat, diquat and difenzoquat by micellar electrokinetic chromatography (MEKC) using sweeping and cation-selective exhaustive injection (CSEI) as on-line concentration methods were developed. Sodium dodecyl sulfate (80 mM) in 50 mM phosphate buffer (pH 2.5) with 20% acetonitrile was used as a background electrolyte for the methods studied. The limits of detection, based on a signal-to-noise ratio of 3:1, were about 2.6-5.1 mg 1(-1) in purified water when MEKC was applied for the standards. By using an on-line preconcentration method known as sweeping-MEKC, up to a 500-fold increase in detection sensitivity was obtained whereas up to a 50 000-fold increase for CSEI-sweeping-MEKC was achieved. The limits of detection using optimum CSEI-sweeping-MEKC were lower than 1 microg 1(-1) and the method was validated obtaining good reproducibility (relative standard deviation lower than 22%) and linearity. CSEI-sweeping-MEKC was successfully applied to the determination of the three herbicides in spiked tap water below the levels established by the US Environmental Protection Agency.

Cations↗
PubMed2001

Anion selective exhaustive injection-sweep-micellar electrokinetic chromatography.

A selective on-line sample concentration technique of anion selective exhaustive injection (ASEI)-sweep-micellar electrokinetic chromatography (MEKC) was evaluated using a cationic surfactant. To suppress the electroosmotic flow, a polyacrylamide-coated capillary was introduced. Some aromatic carboxylic acids, dansyl amino acids, and naphthalene-disulfonic acids were used as test analytes. About 1,000- to 6,000-fold increases in detection sensitivity were obtained in terms of peak heights by ASEI-sweep-MEKC.

Anions↗
PubMed2006

Direct and sensitive analysis of methamphetamine, ketamine, morphine and codeine in human urine by cation-selective exhaustive injection and sweeping micellar electrokinetic chromatography.

Cation-selective exhaustive injection and sweeping micellar electrokinetic chromatography (CSEI-Sweep-MEKC) was directly used to test some abuse drugs in human urine, including morphine (M), codeine (C), ketamine (K) and methamphetamine (MA). First, phosphate buffer (50 mM, pH 2.5) containing 30% methanol was filled into uncoated fused silica capillary (40 cm, 50 microm I.D.), then high conductivity buffer (100 mM phosphate, 6.9 kPa for 99.9 s) was followed. Electrokinetic injection (10 kV, 500 s) was used to load samples and to enhance sensitivity. The stacking step and separation were performed at -20 kV and 200 nm using phosphate buffer (25 mM, pH 2.5) containing 20% methanol and 100 mM sodium dodecyl sulfate. Using CSEI-Sweep-MEKC, the analytes could be simultaneously analyzed and have a detection limit down to ppb level. It was unnecessary to have sample pretreatments. During method validation, calibration plots were linear (r>or=0.9982) over a range of 150-3,000 ng/mL for M and C, 250-5,000 n g/mL for MA, and 50-1,000 ng/mL for K. The limits of detection were 15 ng/mL for M and C, and 5 ng/mL for MA and K (S/N=3, sampling 500 s at 10 kV). Comparing with capillary zone electrophoresis, the results indicated that this stacking method could increase 6,000-fold sensitivity for analysis of MA. Our method was applied for analysis of 28 real urine samples. The results showed good coincidence with immunoassay and GC-MS. This method was feasible for application to detect trace levels of abused drugs in forensic analysis.

Cations↗
PubMed2006

Anion-selective exhaustive injection-sweeping microemulsion electrokinetic chromatography.

In this study, anion-selective exhaustive injection-sweeping (ASEI-sweeping) technique, which is a selective on-line sample concentration technique, was first proposed in microemulsion electrokinetic chromatography (MEEKC) for analyses of eight acidic phenolic compounds. In contrast to a capillary that is typically filled with nonmicellar background solution in conventional ASEI-sweeping MEKC method, in the proposed ASEI-sweeping MEEKC method, a capillary is filled with a low pH microemulsion solution (pH 2.0), and then with a short acid plug (pH 2.0, 1.9 cm) before field-amplified sample injection. This proposed design has two functions. First, the microemulsion solution that is present at the front of capillary column is able to avoid phase separation of microemulsion solution during MEEKC separation. Second, the presence of the short acid plug would effectively limit the partition behavior of acid analytes with the oil droplets in the microemulsion during field-amplified sample injection; otherwise, the stacking effect of acid analytes would be markedly reduced. This optimal ASEI-sweeping MEEKC method afforded about 96,000-fold to 238,000-fold increases in detection sensitivity in terms of peak areas without any separation efficiency loss when compared to normal MEEKC separation. Furthermore, trace levels (about 3 ng/g) of gallic acid and catechin in foods were also detected successfully by the proposed ASEI-sweeping MEEKC technique.

Acids↗
PubMed2006

Selection under domestication: evidence for a sweep in the rice waxy genomic region.

Rice (Oryza sativa) was cultivated by Asian Neolithic farmers >11,000 years ago, and different cultures have selected for divergent starch qualities in the rice grain during and after the domestication process. An intron 1 splice donor site mutation of the Waxy gene is responsible for the absence of amylose in glutinous rice varieties. This mutation appears to have also played an important role in the origin of low amylose, nonglutinous temperate japonica rice varieties, which form a primary component of Northeast Asian cuisines. Waxy DNA sequence analyses indicate that the splice donor mutation is prevalent in temperate japonica rice varieties, but rare or absent in tropical japonica, indica, aus, and aromatic varieties. Sequence analysis across a 500-kb genomic region centered on Waxy reveals patterns consistent with a selective sweep in the temperate japonicas associated with the mutation. The size of the selective sweep (>250 kb) indicates very strong selection in this region, with an inferred selection coefficient that is higher than similar estimates from maize domestication genes or wild species. These findings demonstrate that selection pressures associated with crop domestication regimes can exceed by one to two orders of magnitude those observed for genes under even strong selection in natural systems.

Agriculture↗
PubMed2001

Spectrotemporal sensitivities in rat auditory cortical neurons.

Studies in several mammalian species have demonstrated that auditory cortical neurons respond strongly to single frequency-modulated (FM) sweeps, and that most responses are selective for sweep direction and/or rate. In the present study, we used extracellular recordings to examine how neurons in the auditory cortices of anesthetized rats respond to continuous, periodic trains of FM sweeps (described previously by deCharms et al., Science 280 (1998) pp. 1439-1444, as moving auditory gratings). Consistent with previous observations in owl monkeys, we found that the majority of cortical neurons responded selectively to trains of either up-sweeps or down-sweeps; selectivity for down-sweeps was most common. Periodic responses were typically evoked only by sweep trains with repetition rates less than 12 sweeps per second. Directional differences in responses were dependent on repetition rate. Our results support the proposal that a combination of both spectral and temporal acoustic features determines the responses of auditory cortical neurons to sound, and add to the growing body of evidence indicating that the traditional view of the auditory cortex as a frequency analyzer is not sufficient to explain how the mammalian brain represents complex sounds.

Acoustic Stimulation↗
PubMed2006

Neural mechanisms underlying selectivity for the rate and direction of frequency-modulated sweeps in the auditory cortex of the pallid bat.

Frequency-modulated (FM) sweeps are common in vocalizations, including human speech. Selectivity for FM sweep rate and direction is present in the auditory cortex of many species. The present study sought to determine the mechanisms underlying FM sweep selectivity in the auditory cortex of pallid bats. In the pallid bat inferior colliculus (IC), two mechanisms underlie selectivity for FM sweep rate. The first mechanism depends on duration tuning for tones that arises as a consequence of early inhibition generated by an excitatory tone. The second mechanism depends on a narrow band of delayed high-frequency inhibition. Direction selectivity depends on a broad band of early low-frequency inhibition. Here, the contributions of these mechanisms to cortical FM sweep selectivity were determined in pentobarbital-anesthetized pallid bats. We show that the majority of cortical neurons tuned to echolocation frequencies are selective for the downward direction and rate of FM sweeps. Unlike in IC neurons tuned in the echolocation range, duration tuning is rare in cortical neurons with similar tuning. As in the IC, consistent spectrotemporal differences exist between low- and high-frequency sidebands. A narrow band of delayed high-frequency inhibition is necessary for FM rate selectivity. Low-frequency inhibition has a broad bandwidth, early arrival time, and creates direction selectivity. Cortical neurons respond better to slower FM rates and exhibit broader rate tuning than IC neurons. Relative arrival time of high-frequency inhibition is slower in the cortex than in the IC. Thus whereas similar mechanisms shape direction selectivity of neurons tuned in the echolocation range in the IC and the cortex, only one of the two mechanisms underlying rate selectivity in the IC is present in the cortex.

Acoustic Stimulation↗
PubMed2000

Sample stacking of cationic and anionic analytes in capillary electrophoresis.

The behavior of charged species along concentration boundaries in capillary zone electrophoresis (CZE) that was first described in detail by Everaerts et al. in 1979 assured the possibility of concentrating charged solutes inside the capillary. The concentration effect is based on the sudden change in analyte electrophoretic velocity brought about by the difference in the magnitude of the electric field. Furthermore, this on-line method could be the needed solution to the problem of low concentration sensitivity in CZE. Sample stacking, which is now its well known name, has then found valuable use in applying CZE in many fields, especially after the in-depth studies performed in the early 90s by Chien and Burgi. This article reviews the theory and methodological developments of sample stacking developed for charged analytes in CZE and also in electrokinetic chromatography. A table conveying the reported applications especially in the biomedical and environmental fields is given. On top of this, other on-line concentration methods for charged species, namely, sample self-stacking, acetonitrile stacking, sweeping, cation selective exhaustive injection-sweeping, and use of a pH junction, are briefly discussed.

Anions↗
PubMed2006

Cation-selective exhaustive injection and sweeping MEKC for direct analysis of methamphetamine and its metabolites in urine.

Direct analysis of methamphetamine, amphetamine, and p-hydroxymethamphetamine in urine was achieved by cation-selective exhaustive injection and sweeping micellar EKC. A bare fused-silica capillary (40 cm, 50 microm id) was filled with phosphate buffer (80 mM, pH 3, containing 20% ACN). Then a high-conductivity buffer (100 mM phosphate, pH 3; 6.9 kPa for 2.5 min) was injected. Samples were loaded using electrokinetic injection (10 kV, 600 s) which created long zones of cationic analytes. To enhance sensitivity by sweeping, the stacking step was performed using a phosphate buffer (50 mM, pH 3, containing 20% ACN and 100 mM SDS) at -20 kV before separation by MEKC. This method was capable of detecting the analytes at ppb levels. The calibration plots were linear (r(2) >or= 0.9948) over a range of 100-5000 ng/mL for methamphetamine, and 100-2000 ng/mL for amphetamine and p-hydroxymethamphetamine. The LODs (S/N = 3) were 20 ng/mL for methamphetamine, and 15 ng/mL for amphetamine and p-hydroxymethamphetamine. The method was applied to analysis of 14 urine samples of addicts and is suitable for screening suspected samples for forensic purposes. The results showed good agreement with fluorescence polarization immunoassay and GC-MS.

Amphetamine↗
PubMed2000

Determination of environmentally relevant aromatic amines in the ppt levels by cation selective exhaustive injection-sweeping-micellar electrokinetic chromatography.

Environmentally important aromatic amines are determined by micellar electrokinetic chromatography (MEKC) with UV detection. Using a combination of field-enhanced sample injection in the capillary zone electrophoresis format (performed for a longer period than usual, e.g., 200 s at high voltages; cation selective exhaustive injection) and sweeping in the MEKC format, from 10(4)- to 10(5)-fold improvements in detector response are achieved for all positively chargeable test analytes. Preliminary results indicate that limits of detection for the positively chargeable aromatic amines are in the parts per trillion (ppt) levels.

Amines↗
PubMed2000

Approaching a million-fold sensitivity increase in capillary electrophoresis with direct ultraviolet detection: cation-selective exhaustive injection and sweeping

A novel method that combines two on-line concentration techniques in capillary electrophoresis (CE), namely, sample stacking with electrokinetic injection (field-enhanced sample injection, FESI) and sweeping, afforded the detection of positively chargeable analytes in parts per trillion (ppt) levels. The main idea is to selectively introduce by FESI as many molecules of cationic analytes as possible from a very dilute sample solution and focus the resulting zone by sweeping. Limit of detection values (signal-to-noise ratio 3) of 4.1 and 8.0 ppt-the lowest concentration reported by direct UV detection in CE-with average plate numbers of 3.6 x 10(5) and 4.4 x 10(5) are obtained for laudanosine and naphthylamine (standard solutions), respectively. This translates to improvements in peak heights compared with usual injection approaching a million-fold. Optimization schemes and application to quantitative and qualitative analyses are also investigated.

Journal Article↗
PubMed2005

On the prediction of sweep rate and directional selectivity for FM sounds from two-tone interactions in the inferior colliculus.

Two-tone stimuli have traditionally been used to reveal regions of inhibition in auditory spectral receptive fields, particularly for neurons with low spontaneous rates. These techniques reveal how different frequencies excite or suppress the response to an excitatory frequency of a cell, but have often been assessed at a fixed masker-probe time interval. We used a variation of this methodology to determine whether two-tone spectrotemporal interactions can account for rate-dependent directional selectivity for frequency modulations (FM) in the mustached bat inferior colliculus (IC). First, we quantified the response to upward and downward sweeping, linear, fixed-bandwidth FM tones centered at a unit's characteristic frequency (CF) at 6 sweep durations ranging from 2 to 64 ms. Then, to examine how responses to instantaneous frequencies contained within the sweeps might interact in time, we varied the frequency and relative onset of a brief (4 ms) "conditioner" tone paired with a fixed 4-ms CF probe tone. We constructed "conditioned response areas" (CRA) depicting regions of suppression and facilitation of the probe tone caused by the conditioning tone. We classified the CRAs as predominantly excitatory (40.9%), inhibitory (22.7%), or mixed (36.4%). To generate FM response predictions, the CRAs were multiplied with spectrograms of the same sweeps used to assess response to FM. The predictions of FM rate and directionality were accurate by our criteria in approximately 20% of units. Conversely, the CRAs from the remaining units failed to predict FM responses as accurately, suggesting that most IC units respond differently to FM sweeps than they do to tone-pairs matched to the instantaneous frequencies contained in those sweeps. The implications of these results for models of FM directionality are discussed.

Acoustic Stimulation↗